4DMU

Crystal structure of the von Willebrand factor A3 domain in complex with a collagen III derived triple-helical peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	vWA-like	8032262	3000832	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	vWA-like	8032262	3000832	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	vWA-like	8032262	3000832	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	vWA-like	8032262	3000832	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	vWA-like	8032262	3000832	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	vWA-like	8032262	3000832	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	VWA	e4dmuB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
D	VWA	e4dmuD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
F	VWA	e4dmuF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
H	VWA	e4dmuH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
J	VWA	e4dmuJ1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
L	VWA	e4dmuL1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
D	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
F	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
H	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
J	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
L	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	von Willebrand factor	protein binding binding enzyme binding protease binding collagen binding protein-containing complex binding protein-folding chaperone binding cell adhesion molecule binding integrin binding signaling receptor binding immunoglobulin binding identical protein binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding cell activation cellular process platelet activation multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding cell activation cellular process platelet activation cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process positive regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication signal transduction positive regulation of cellular process positive regulation of signaling cell adhesion cell-substrate adhesion	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle Weibel-Palade body secretory granule clathrin-coated vesicle secretory vesicle coated vesicle cytoplasm platelet alpha granule vesicle lumen membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen organelle lumen platelet alpha granule lumen endoplasmic reticulum
A, C, E, G, I A, C, E, G, I, K	Collagen III derived triple-helical peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR050780	Mucin/von Willebrand/Thrombospondin superfamily	Family
B, D, F, H, J B, D, F, H, J, L	IPR002919	Trypsin Inhibitor-like, cysteine rich domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR001007	VWFC domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR037578	Von Willebrand factor	Family
B, D, F, H, J B, D, F, H, J, L	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR001846	von Willebrand factor, type D domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR014853	VWF/SSPO/Zonadhesin-like, cysteine-rich domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR032361	von Willebrand factor, VWA N-terminal domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR036084	Serine protease inhibitor-like superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR002035	von Willebrand factor, type A	Domain
B, D, F, H, J B, D, F, H, J, L	IPR006207	Cystine knot, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L	Pharos: P04275	von Willebrand disease 1 von Willebrand disease 2 von Willebrand disease 3 atrial fibrillation hypertensive disorder hereditary von Willebrand disease thrombotic disease intracranial thrombosis Liver Cirrhosis, Experimental cardiovascular disease congestive heart failure ovarian cancer Down syndrome pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia drug-induced liver injury von Willebrand disease 1 von Willebrand disease 2 von Willebrand disease 3 atrial fibrillation hypertensive disorder hereditary von Willebrand disease thrombotic disease intracranial thrombosis Liver Cirrhosis, Experimental cardiovascular disease congestive heart failure ovarian cancer Down syndrome pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia drug-induced liver injury peripheral neuropathy gastric carcinoma thrombocytopenia heart failure acquired von willebrand syndrome herpes zoster transitional cell carcinoma interstitial cystitis kidney disease von Willebrand disease type 2A lung adenocarcinoma von Willebrand disease type 2N non-small cell lung carcinoma coronary artery disease pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ thrombophilia thrombotic thrombocytopenic purpura adrenal cortex carcinoma ulcerative colitis angiodysplasia Bernard-Soulier syndrome von Willebrand disease type 2B breast carcinoma lung cancer medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm peripheral nervous system disease familial atrial fibrillation pulmonary embolism heart disease hemophilia A inborn carbohydrate metabolic disorder vascular disease atherosclerosis invasive ductal breast carcinoma von Willebrand disease type 2M lung carcinoma cerebrovascular disorder

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E, G, I A, C, E, G, I, K	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
A, C, E, G, I A, C, E, G, I, K	HYP	Parent Component: PRO RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0030 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 , 4-hydroxy-L-proline MOD:00039
A, C, E, G, I A, C, E, G, I, K	NH2	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0030 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 , 4-hydroxy-L-proline MOD:00039 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.